💡 Quick Summary

PCR Products accepts one or more DNA template sequences and two primer sequences, then finds all PCR products that the primers can generate. Products are sorted by size and reported in FASTA format with their position, length, and the primers that produced them.

📋 How to Use

Paste one or more DNA template sequences (raw or FASTA) into the template area. Multiple FASTA sequences each get their own title line.
Enter the name and sequence (5′→3′) for each primer. Both primers must be at least 10 bases long.
Choose the template topology: Linear (default) or Circular (for plasmids and other circular molecules).
Click Submit. Products are reported in FASTA format, sorted from largest to smallest.
Click Load Example to run T7 and T3 primers against a sample pUC19 sequence.
Use Copy All to copy the FASTA output to your clipboard.

🧮 Formulas & Logic

Product detection

Each primer is matched to the forward strand and the reverse complement strand using exact regex matching (IUPAC degenerate bases expanded to character classes).

Product boundaries

Start = first base of the forward-strand primer match. Stop = last base of the reverse-strand primer match (reverse complement position).

Circular products

For circular templates, the search region is extended by 50 bp at each end to detect products that span the sequence origin.

Sort order

Products sorted largest → smallest by sequence length.

📊 Result Interpretation

Product size

Shown in bp in the FASTA header. Includes both primer sequences.

Base range

"base X to base Y" is 1-based, inclusive, relative to the input template sequence.

Primer labels

Shows which primer matched the forward strand and which matched the reverse strand.

🔬 Applications

Predicting PCR product sizes before running a gel
Verifying primer placement in a cloning vector or genomic sequence
Checking for unintended off-target products from degenerate primers
Confirming that primers flank an insert in a circular plasmid
Designing diagnostic PCR assays and predicting band patterns

⚠️ Common Mistakes & Warnings

Exact match only — no mismatches

The tool finds only perfectly matching primer sites. Use IUPAC degenerate bases (R, Y, N, etc.) in primer sequences to allow mismatches at specific positions.

Both primers can bind to either strand

Each primer is searched on both the forward strand and the reverse complement. A product is reported whenever two primer binding sites face each other, regardless of which primer is which.

Primers must be ≥ 10 bases

Very short primers produce too many non-specific matches to be useful.

Template input limit: 2,000,000 characters

Each template sequence (after stripping non-DNA characters) can be up to 2 Mb.

❓ Frequently Asked Questions

Why does the tool find products using either primer as the "forward" primer?

Both primers are searched on both strands. A product is formed whenever one primer matches the top strand and the other matches the bottom strand (reverse complement) at compatible positions. This correctly handles cases where a primer could amplify in more than one direction.

I expected a product but nothing was found. Why?

The tool requires a perfect sequence match (allowing only the degenerate bases you specify). Check that the primer sequence exactly matches the template, including orientation — primers are entered 5′→3′ and the tool handles both strands automatically.

What does "circular" topology change?

For circular molecules, the tool extends the search region at both ends so it can detect products that span the arbitrary start/end position in the sequence.

The product size seems larger than expected. What's included?

Product sequences include both complete primer binding sites (from the first base of the forward primer to the last base of the reverse primer). This is the experimentally amplified product, matching what you would see on a gel.